The captain of the foreign-flagged ship chartered for the aluminium company Alcoa to replace its Australian vessel paid bribes to drug enforcement and immigration authorities in Nigeria and a shipping inspector in Argentina early this year, the former captain's own documents show.

The international seafarers' union has forwarded the documents to the Australian Federal Police for investigation.

Maritime unions have also called on Deputy Prime Minister Warren Truss to suspend immediately the federal government's special licence allowing Alcoa to replace its Australian ship and crew with the Singapore-registered vessel, the Strategic Alliance.

The Australian national co-ordinator of the International Transport Workers Federation, Dean Summers, said there were "obvious security implications for Australia if this company's business model includes systematic bribery of government officials and drug crime agencies".

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Deputy Prime Minister Warren TrussCredit:Alex Ellinghausen

A spokesman for the ship's management company denied it practised bribery, and said the former captain had paid the "under the table" money "without our knowledge".

However, the assistant national secretary of the Maritime Union of Australia, Ian Bray, predicted corruption would prove "just the tip of the iceberg" if coastal shipping were to be further deregulated.

"Mr Truss must revoke this licence immediately," he said.

A document identified as "captain's statement of account" for the Strategic Alliance, covering January, 2015, was among papers retrieved by inspectors from the ITF who went aboard the ship in Portland on Sunday, according to Mr Summers.

One of the documents forwarded to the AFP for investigation.

The statement details payments described as "under table money" to Nigeria's drug law enforcement agency and to Nigerian immigration authorities.

It also states that thousands of US dollars of "under table money" were paid to a "hold inspector" later that month in the Argentinian port of Necochea.

It does not explain why these "under table" payments – the universal code for bribes – were made to immigration authorities ($US500 in Port Harcourt, Nigeria) or a ship's hold inspector ($US3500 in the port of Necochea, Argentina).

An entry for $400 "under table money to NDLEA" in Port Harcourt, Nigeria, is explained as "for clearance". The NDLEA is identified in a handwritten addendum to the captain's statement of account as the National Drug Law Enforcement Agency (Nigeria).

Also unexplained is an entry for $US150 to purchase a Chilean flag in Argentina, despite the ship being registered under the flag of Singapore.

The document, which contains two indecipherable signatures, appears under the heading MTM Ship Management Pte Ltd.

MTM, headquartered in Singapore, manages 45 vessels on behalf of ship owners in the US, Japan, Hong Kong, Indonesia and the UK. The company's website boasts that "our inspiration is drawn from the ant, which goes about its business quietly, carrying twice its body weight and planning for the season ahead".

An MTM technical supervisor in charge of the Strategic Alliance contract, Mr Robert Viro, told Fairfax Media on Monday that the bribes paid by the captain had been "done without our knowledge".

He said the captain, from Myanmar, had since left the company's fleet, and the current captain of the Strategic Alliance was from The Philippines.

Alcoa is scrapping its ship, the MV Portland, which has hauled alumina from Western Australia to the Portland aluminium smelter in far-west Victoria for the past 27 years.

It is being replaced on the route by the US-owned and Singapore-registered Strategic Alliance, which has a crew of Filipinos each being paid about $US150 ($207) a week. Alcoa says this will save the aluminium company $6 million a year.

The 40 Australian crew members of the MV Portland have been refusing for more than three weeks to sail the ship from Portland to Singapore, where they are to be made redundant.

The Strategic Alliance was moored a few hundred metres from the MV Portland on Monday at Alcoa's Portland berth after steaming from Kwinana, Western Australia, with its first cargo of alumina under the special "temporary coastal licence" issued by the government in late October.

Senators from all sides of politics expressed disbelief on Friday when senior officials from the Department of Infrastructure and Regional Development, which enforces the Coastal Trading Act, revealed they did not feel there was a need to check the ownership of ships plying the Australian coast.

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"I don't care who is in government, I think we're entitled to know who the bloody hell we're dealing with. Jesus, I can't believe that," Liberal senator Bill Heffernan exploded at the inquiry into shipping Flags of Convenience.